protocols::simple_filters::RelativePoseFilter Class Reference

#include <RelativePoseFilter.hh>

Public Member Functions
	RelativePoseFilter ()
	default ctor More...
virtual bool	apply (core::pose::Pose const &pose) const
	Constructor with a single target residue. More...
virtual void	report (std::ostream &out, core::pose::Pose const &pose) const
virtual core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...
virtual protocols::filters::FilterOP	clone () const
virtual protocols::filters::FilterOP	fresh_instance () const
core::Real	compute (core::pose::Pose const &pose) const
virtual	~RelativePoseFilter ()
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
void	filter (protocols::filters::FilterOP filter)
protocols::filters::FilterOP	filter () const
protocols::moves::MoverOP	relax_mover () const
void	relax_mover (protocols::moves::MoverOP const mover)
core::pose::PoseOP	pose () const
void	pose (core::pose::PoseOP p)
void	pdb_name (std::string const pdb_name)
std::string	dump_pose_fname () const
void	dump_pose_fname (std::string const s)
core::scoring::ScoreFunctionOP	scorefxn () const
void	scorefxn (core::scoring::ScoreFunctionOP const s)
void	packing_shell (core::Real const s)
core::Real	packing_shell () const
core::pose::PoseOP	thread_seq (core::pose::Pose const &p) const
bool	thread () const
void	thread (bool const t)
bool	baseline () const
void	baseline (bool const b)
core::Real	baseline_val () const
void	baseline_val (core::Real const )
bool	unbound () const
void	unbound (bool const b)
bool	copy_stretch () const
void	copy_stretch (bool const b)
void	symmetry_definition (std::string const s)
std::string	symmetry_definition () const
std::string	filter_name () const
void	filter_name (std::string const s)
void	rtmin (bool const b)
bool	rtmin () const
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	Filter (Filter const &)
virtual	~Filter ()
virtual std::string	get_type () const
std::string	get_user_defined_name () const
void	set_user_defined_name (std::string const &name)
virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
virtual void	apply (core::io::serialization::PipeMap &pmap)
virtual void	score (core::io::serialization::PipeMap &pmap)
virtual core::Real	score (core::pose::Pose &pose)
virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
virtual std::string	name () const

Private Types
typedef protocols::filters::Filter	parent

Private Attributes
protocols::filters::FilterOP	filter_
protocols::moves::MoverOP	relax_mover_
std::map< core::Size, core::Size >	alignment_
std::string	dump_pose_fname_
core::pose::PoseOP	pose_
core::scoring::ScoreFunctionOP	scorefxn_
core::Real	packing_shell_
bool	thread_
bool	baseline_
core::Real	baseline_val_
bool	unbound_
bool	copy_stretch_
std::string	symmetry_definition_
core::conformation::symmetry::SymmDataOP	symmdata_
std::string	filter_name_
bool	rtmin_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Member Typedef Documentation

typedef protocols::filters::Filter protocols::simple_filters::RelativePoseFilter::parent

private

Constructor & Destructor Documentation

protocols::simple_filters::RelativePoseFilter::RelativePoseFilter

(

)

default ctor

References alignment_.

Referenced by clone(), protocols::simple_filters::RelativePoseFilterCreator::create_filter(), and fresh_instance().

protocols::simple_filters::RelativePoseFilter::~RelativePoseFilter ( )

virtual

Member Function Documentation

bool protocols::simple_filters::RelativePoseFilter::apply ( core::pose::Pose const &  pose ) const

virtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

References filter(), and thread_seq().

bool protocols::simple_filters::RelativePoseFilter::baseline

(

)

const

References baseline_.

Referenced by baseline_val(), compute(), parse_my_tag(), and thread_seq().

void protocols::simple_filters::RelativePoseFilter::baseline

(

bool const

b

)

References protocols::match::upstream::b, and baseline_.

core::Real protocols::simple_filters::RelativePoseFilter::baseline_val

(

)

const

References baseline(), baseline_val_, and runtime_assert.

Referenced by compute(), parse_my_tag(), and thread_seq().

void protocols::simple_filters::RelativePoseFilter::baseline_val

(

core::Real const

b

)

References protocols::match::upstream::b, baseline(), baseline_val_, and runtime_assert.

protocols::filters::FilterOP protocols::simple_filters::RelativePoseFilter::clone ( ) const

virtual

Implements protocols::filters::Filter.

References RelativePoseFilter().

core::Real protocols::simple_filters::RelativePoseFilter::compute

(

core::pose::Pose const &

pose

)

const

References protocols::simple_moves::DumpPdb::apply(), baseline(), baseline_val(), dump, dump_pose_fname(), filter(), filter_name(), report_sm(), scorefxn(), protocols::simple_moves::DumpPdb::set_scorefxn(), thread_seq(), and protocols::simple_filters::TR.

Referenced by report_sm().

bool protocols::simple_filters::RelativePoseFilter::copy_stretch ( ) const

inline

References copy_stretch_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::simple_filters::RelativePoseFilter::copy_stretch ( bool const  b )

inline

References protocols::match::upstream::b, and copy_stretch_.

std::string protocols::simple_filters::RelativePoseFilter::dump_pose_fname

(

)

const

References dump_pose_fname_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_filters::RelativePoseFilter::dump_pose_fname

(

std::string const

s

)

References dump_pose_fname_.

void protocols::simple_filters::RelativePoseFilter::filter

(

protocols::filters::FilterOP

filter

)

References filter(), and filter_.

protocols::filters::FilterOP protocols::simple_filters::RelativePoseFilter::filter

(

)

const

References filter_.

Referenced by apply(), compute(), filter(), and parse_my_tag().

std::string protocols::simple_filters::RelativePoseFilter::filter_name

(

)

const

References filter_name_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_filters::RelativePoseFilter::filter_name

(

std::string const

s

)

References filter_name_.

protocols::filters::FilterOP protocols::simple_filters::RelativePoseFilter::fresh_instance ( ) const

virtual

Implements protocols::filters::Filter.

References RelativePoseFilter().

void protocols::simple_filters::RelativePoseFilter::packing_shell

(

core::Real const

s

)

References packing_shell_.

core::Real protocols::simple_filters::RelativePoseFilter::packing_shell

(

)

const

References packing_shell_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::simple_filters::RelativePoseFilter::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data, protocols::filters::Filters_map const &  filters, protocols::moves::Movers_map const &  movers, core::pose::Pose const &  p  )

virtual

alignment is expecting X1:Y1,X2:Y2,X3:Y3... where X is the protein on disk (target) and Y is the active structure (starting structure). When no alignment is given it is implied that the poses are trivially aligned 1..nres Feb2012 added option to align entire chains: A:B,D:C. Notice that no testing is made to ensure correct lengths etc., simply aligns from the start to end of the chains sequentially.

Reimplemented from protocols::filters::Filter.

References alignment_, protocols::moves::Mover::apply(), baseline(), baseline_val(), copy_stretch(), dump_pose_fname(), core::pose::symmetry::extract_asymmetric_unit(), filter(), filter_name(), core::pose::symmetry::is_symmetric(), length, core::pose::symmetry::make_symmetric_pose(), core::pose::Pose::n_residue(), basic::options::OptionKeys::in::file::native, core::pose::Pose::num_jump(), basic::options::option, packing_shell(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), core::pose::parse_resnum(), protocols::rosetta_scripts::parse_score_function(), core::pose::Pose::pdb_info(), pdb_name(), pose(), pose_, core::import_pose::pose_from_pdb(), relax_mover(), report_sm(), residues, rtmin(), runtime_assert, scorefxn(), utility::string_split(), symmdata_, symmetry_definition_, thread(), core::pose::Pose::total_residue(), protocols::simple_filters::TR, and unbound().

void protocols::simple_filters::RelativePoseFilter::pdb_name

(

std::string const

pdb_name

)

References pose(), and core::import_pose::pose_from_pdb().

Referenced by parse_my_tag().

core::pose::PoseOP protocols::simple_filters::RelativePoseFilter::pose

(

)

const

References pose_.

Referenced by parse_my_tag(), pdb_name(), pose(), and thread_seq().

void protocols::simple_filters::RelativePoseFilter::pose

(

core::pose::PoseOP

p

)

References pose(), and pose_.

protocols::moves::MoverOP protocols::simple_filters::RelativePoseFilter::relax_mover

(

)

const

References relax_mover_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::simple_filters::RelativePoseFilter::relax_mover

(

protocols::moves::MoverOP const

mover

)

References relax_mover_.

void protocols::simple_filters::RelativePoseFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

virtual

Reimplemented from protocols::filters::Filter.

core::Real protocols::simple_filters::RelativePoseFilter::report_sm ( core::pose::Pose const &  ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

Referenced by compute(), and parse_my_tag().

void protocols::simple_filters::RelativePoseFilter::rtmin

(

bool const

b

)

References protocols::match::upstream::b, and rtmin_.

bool protocols::simple_filters::RelativePoseFilter::rtmin

(

)

const

References rtmin_.

Referenced by parse_my_tag(), and thread_seq().

core::scoring::ScoreFunctionOP protocols::simple_filters::RelativePoseFilter::scorefxn

(

)

const

References scorefxn_.

Referenced by compute(), parse_my_tag(), scorefxn(), and thread_seq().

void protocols::simple_filters::RelativePoseFilter::scorefxn

(

core::scoring::ScoreFunctionOP const

s

)

References scorefxn(), and scorefxn_.

void protocols::simple_filters::RelativePoseFilter::symmetry_definition

(

std::string const

s

)

References symmetry_definition_.

std::string protocols::simple_filters::RelativePoseFilter::symmetry_definition

(

)

const

References symmetry_definition_.

bool protocols::simple_filters::RelativePoseFilter::thread

(

)

const

References thread_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::simple_filters::RelativePoseFilter::thread

(

bool const

t

)

References thread_.

core::pose::PoseOP protocols::simple_filters::RelativePoseFilter::thread_seq

(

core::pose::Pose const &

p

)

const

References core::conformation::Residue::aa(), alignment_, protocols::moves::Mover::apply(), protocols::rigid::RigidBodyTransMover::apply(), baseline(), baseline_val(), core::pose::Pose::conformation(), core::pose::Pose::copy_segment(), copy_stretch(), core::conformation::Conformation::detect_disulfides(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::name1(), num_canonical_aas, packing_shell(), pose(), relax_mover(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), residue, rtmin(), scorefxn(), protocols::rigid::RigidBodyTransMover::step_size(), tf, thread(), core::pose::Pose::total_residue(), protocols::simple_filters::TR, and unbound().

Referenced by apply(), and compute().

bool protocols::simple_filters::RelativePoseFilter::unbound ( ) const

inline

References unbound_.

Referenced by parse_my_tag(), and thread_seq().

void protocols::simple_filters::RelativePoseFilter::unbound ( bool const  b )

inline

References protocols::match::upstream::b, and unbound_.

Member Data Documentation

std::map< core::Size, core::Size > protocols::simple_filters::RelativePoseFilter::alignment_

private

Referenced by parse_my_tag(), RelativePoseFilter(), and thread_seq().

bool protocols::simple_filters::RelativePoseFilter::baseline_

private

Referenced by baseline().

core::Real protocols::simple_filters::RelativePoseFilter::baseline_val_

private

Referenced by baseline_val().

bool protocols::simple_filters::RelativePoseFilter::copy_stretch_

private

Referenced by copy_stretch().

std::string protocols::simple_filters::RelativePoseFilter::dump_pose_fname_

private

Referenced by dump_pose_fname().

protocols::filters::FilterOP protocols::simple_filters::RelativePoseFilter::filter_

private

Referenced by filter().

std::string protocols::simple_filters::RelativePoseFilter::filter_name_

private

Referenced by filter_name().

core::Real protocols::simple_filters::RelativePoseFilter::packing_shell_

private

Referenced by packing_shell().

core::pose::PoseOP protocols::simple_filters::RelativePoseFilter::pose_

private

Referenced by parse_my_tag(), and pose().

protocols::moves::MoverOP protocols::simple_filters::RelativePoseFilter::relax_mover_

private

Referenced by relax_mover().

bool protocols::simple_filters::RelativePoseFilter::rtmin_

private

Referenced by rtmin().

core::scoring::ScoreFunctionOP protocols::simple_filters::RelativePoseFilter::scorefxn_

private

Referenced by scorefxn().

core::conformation::symmetry::SymmDataOP protocols::simple_filters::RelativePoseFilter::symmdata_

private

Referenced by parse_my_tag().

std::string protocols::simple_filters::RelativePoseFilter::symmetry_definition_

private

Referenced by parse_my_tag(), and symmetry_definition().

bool protocols::simple_filters::RelativePoseFilter::thread_

private

Referenced by thread().

bool protocols::simple_filters::RelativePoseFilter::unbound_

private

Referenced by unbound().

---

The documentation for this class was generated from the following files:

• symlinks/rosetta/src/protocols/simple_filters/RelativePoseFilter.hh
• symlinks/rosetta/src/protocols/simple_filters/RelativePoseFilter.cc